Professor Nagasaki will give a lecture at the 2nd NHRI-ToMMo Conference “Genomics, Biobanking, and Learning Health Systems” on July 15.
・Date: July 15 (Fri) 13:15-13:45
・Venue: Theater, School of Medicine Building 6, Tohoku University
・Session: Panel 2 Genomics and Omics
・Title: Two thousand Japanese whole genome reference panel in Japan and Bioinformatics
Professor Nagasaki will give a lecture at the 1st meeting of the Japonica Array Society on May 14.
・Date/Time: May 14 (Saturday) 13:30-17:00
・Venue: Head-office building of Toshiba Corporation
・Title: ジャポニカアレイ®と今後の展望
Professor Nagasaki delivered a lecture at The 4th International Symposium on Bioinformatics for Next Generation Sequencing with Applications in Human Genetics on April 2
・Date: April 2 (Saturday), 2016
・Venue: Memorial Auditorium, Kyoto University Faculty of Medicine
・Title: Two thousand whole-genome reference panel and towards optimized reference genome in Japan
The73nd In Silico Megabank Research Seminar will be held on Friday, February 12, 2016. This Time, we will be welcoming Dr. Yuki Hitomi, Graduate School of Medicine, The University of Tokyo as our lecturer, and he will be speaking on “Search for Genetic Factors of Immune-related Diseases”.
・Date/Time: February 12 (Friday) 5:00 pm‐6:30 pm
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Search for Genetic Factors of Immune-related Diseases
・Lecturer: Yuki Hitomi （Department of Human Genetics, Graduate School of Medicine, The University of Tokyo）
＊This lecture is transferable as a class in the medical research-related lecture course.
・Abstract: Genome-wide Association Study (GWAS) has been conducted in large scale globally especially as a statistical genetic approach that exhaustively search disease sensitive genes for multifactorial diseases. On the other hand, it is known that there is genetic risk, Missing Heritability, which is unaccountable with GAWS. Therefore, further advancement of research is currently highly anticipated for understanding of whole genetic factors for disease onset. In this seminar, diseases that are considered to be attributable to immune system being the target, we will give an outline of genetic factors which have been revealed until today (especially HLA) as well as the pathologies. Additionally, we will introduce joint-research having been conducted with ToMMo for the purpose of exhaustive search for genetic factors in association with the development of Primary biliary cirrhosis (PBC) and Stevens-Johnson Syndrome (SJS)
・Organizer: Kaname Kojima, Masao Nagasaki
The 72nd In Silico Megabank Research Seminar will be held on Tuesday, January 26, 2016. This Time, we will be welcoming Dr. Ryu Takeda, The Institute of Scientific and Industrial Research, Osaka University as our lecturer, and he will be speaking on “Recent Machine Learning and Component Technology for Speech Dialog System”.
・Date/Time: January 26 (Tuesday) 5:00 pm‐6:30 pm
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Recent Machine Learning and Component Technology for Speech Dialog System
・Lecturer: Ryu Takeda（The Institute of Scientific and Industrial Research, Osaka University）
＊This lecture is transferable as a class in the medical research-related lecture course.
・Abstract: A speech dialog system is a system that understands and corresponds to human voice questioning to it. Such system is applied to the interface of mobile terminals (Siri), robots (Pepper), and so on. At our laboratory, we conduct studies focusing not only on the linguistic understanding of user speech but on hierarchical understanding of speech behavior and mutual adaptation between system and user. For these types of studies machine learning is an inevitable technology, and it is widely used from signal processing, and voice recognition to the core dialog strategy and user model learning. In this seminar, challenges and necessary technologies for speech dialog system and application of machine learning technology including our study cases will be introduced. In addition, examples of the application of recent Deep Learning in component technology and my approaches and efforts are also introduced.
・Organizer: Kaname Kojima, Masao Nagasaki
The 71st In Silico Megabank Research Seminar will be held on Friday, January 22, 2016. This Time, we will be welcoming Dr. Masahiro Kasahara, Graduate School of Frontier Sciences, The University of Tokyo as our lecturer, and he will be speaking on “Information Processing Technology for Genomic Sequencing”.
・Date/Time: January 22 (Friday) 5:00 pm‐6:30 pm
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Information Processing Technology for Genomic Sequencing
・Lecturer: Masahiro Kasahara（Graduate School of Frontier Sciences, The University of Tokyo）
＊This lecture is transferable as a class in the medical research-related lecture course.
・Abstract: Whole Genome Shotgun Method using PacBio RS, which is the world’s fist real-time single-molecule DNA sequencer for commercial use, is on the verge of becoming the de facto standard as the method to determine genomic sequencing in highly efficient and highly accurate manner. However, in comparison to the previous DNA sequencers, the read length is larger by one digit and the read error rate for base is higher by one digit or more. Thus, it has been difficult to perform genome assembly for large genomes by fully utilizing output information. In this lecture, the advancement of information processing technology to perform genome assembly, especially the error-correction techniques for base and the invention of data structure to correspond to large genomes will be introduced. In addition, the movement of germinating genomic sequencing technology using new observation technologies other than PacBio is to be introduced.
・Organizer: Tomoko Shibata, Masao Nagasaki
The 69th In Silico Megabank Research Seminar will be held on Tuesday, January 12, 2016. This Time, we will be welcoming Dr. Gen Sobue, Nagoya University Graduate School of Medicine as our lecturer, and he will be speaking on “Search for amyotrophic lateral sclerosis pathologically related genes using Japanese genome”.
・Date/Time: January 12 (Tuesday) 3:30 pm‐5:00 pm
・Venue: Conference Room(3rd Floor), Tohoku Medical Megabank Building
・Title: Search for amyotrophic lateral sclerosis pathologically related genes using Japanese genome
・Lecturer: Gen Sobue（Nagoya University Graduate School of Medicine）
＊This lecture is transferable as a class in the medical research-related lecture course.
・Abstract: Amyotrophic lateral sclerosis (ALS) is an intractable neurological disease that requires permanent wearing of a respirator or results in death after a few years from its onset due to worsening muscular atrophy and worsening muscle weakness caused by the altered decidual of motor neurons. About 10% of ALS patients are thought to have a monogenic disease and multiple causative genes are identified; however, the pathologically related genes or molecules for the vast majority of sporadic ALSs are not yet fully revealed. It is necessary to identify sporadic ALS pathologically related genes and molecules in order for the pathophysiological analysis and the development of treatment methods. We have developed a JaCALS which is the multi-institutional joint registry system of ALS patients and accumulated prospective clinical information, genomic DNA, and immortalized lymphocytes of 1140 ALS patients. Also, utilizing this resource, we have produces some results such as the identification of ZNF512B as a sporadic ALS pathologically related gene and the indication that low expression of Titin is related to rapidly progressive sporadic ALS by conducting genome-wide association studies (GWAS) based on Single Nucleotide Polymorphisms (SNPs).
In recent years multiple rare variants hypothesis, where numbers of variants with low allele frequency and uncommon SNPs are contributing to the pathophysiology of sporadic diseases, has been proposed. The purpose of this study is to identify sporadic ALS related variants through association studies using sporadic ALS genome of JaCALS and control at Tohoku Medical Megabank Organization. It is expected that the analysis of exome sequencing of 750 sporadic ALS patients will be complete by the end of this year, which means that we are well established enough to start association study smoothly. If any sporadic ALS related gene is found as a result of the study, we plan to proceed with the preparation of disease model, pathophysiological analysis, and treatment agent screening by iPS cell generation from patient with specific genotype.
・Organizer: Masao Nagasaki
The 70th In Silico Megabank Research Seminar will be held on Friday, January 15, 2016. This Time, we will be welcoming Dr. Fumihiko Takeuchi, Research Institute, National Center for Global Health and Medicine as our lecturer, and he will be speaking on “Genome-wide Association Study (GWAS)”.
・Date/Time: January 15 (Friday) 5:00 pm‐6:30 pm
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Genome-wide Association Study (GWAS): Successful Increase in Scalability for Multi-ethnic Groups and Concerns about Area Difference
・Lecturer: Fumihiko Takeuchi（Research Institute, National Center for Global Health and Medicine）
＊This lecture is transferable as a class in the medical research-related lecture course.
・Abstract: With regard to bio-architecture shown as “DNA−RNA−Protein−Cell−Tissue−Organ−Individual Organism,” genome that DNA codes and diseases representing the health condition of individual organism position at both ends; however, genome study for human diseases is a potent approach to examine diseases and develop treatments. The reason for this possibility is that the relations between genomic variation and diseases can be statistically analyzed (association study) and statistical findings suggest their causal links. In this seminar, large-scale analysis on multi-ethnic groups that enhances the statistical power and area differences in genome which can be a cofounder in association study are introduced.
1. Large-scale GWAS on Blood Pressure
GWAS on blood pressure was conducted targeting Europeans and North Americans, East Asians, South Asians totaling 320,251 participants; 12 related genetic loci were newly identified. Many blood pressure-related SNPs were related to methylation of nearby CpG cites, which suggested that the genomic relations between SNPs and blood pressure are formed by way of methylation.
2. Area Differences in Genes among Japanese People
As an Asian variation project, 34 Asian populations including 8 Japanese populations totaling 3928 participants were analyzed. SNPs information of whole genome enabled categorization of Japanese populations into 9 clusters, and each cluster corresponded to certain areas in Japan. The impact of cluster must be examined as needed for disease association studies.
・Organizer: Yumi Yamaguchi, Masao Nagasaki
The 67th In Silico Megabank Research Seminar will be held on Friday, December 11.
This Time, we will be welcoming Dr. Kazuhiro Nakayama, Center for Molecular Medicine, Jichi Medical University as our lecturer, and he will be speaking on “Construction of Visceral Adipose Genome Bank and its Use”.
・Date/Time: December 11 (Friday) 5:00 pm‐6:30 pm
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Construction of Visceral Adipose Genome Bank and its Use
・Lecturer: Kazuhiro Nakayama（Center for Molecular Medicine, Jichi Medical University ）
＊This lecture is transferable as a class in the medical research-related lecture course.
・Abstract: Visceral adipose is white adipose tissue existing around peritoneum. Visceral adipose evokes various metabolic abnormalities such as hepatic dysfunctions, dyslipidemia, hypertension, hyperuricaemia, and impaired glucose tolerance by actively excreting free fatty acid and cytokine. The heritability of visceral obesity is partially independent from the heritability of subcutaneous fat accumulation; the identification of specifically-attributable genetic polymorphism hasn’t progressed very much yet. Understanding of the genetic background of visceral fat accumulation may contribute to pathophysiological analysis of various chronic diseases that are lead by it. Our group collected genomic DNA and the result data of various health check items such as visceral fat area of periumbilical region, serum lipid level, and existence of fatty liver from 3013 adults who had general multiphasic health screening at Jichi Medical University Hospital and then constructed visceral adipose genome bank. In this seminar, the relationship between Tribbles Pseudokinase family gene and lifestyle diseases which were revealed from the analysis of this genome bank and outcomes so far found are introduced.
・Organizer: Kazuharu Misawa, Masao Nagasaki
The 66th In Silico Megabank Research Seminar will be held on Tuesday, December 8. This Time, we will be welcoming Dr. Wojciech Makalowski, University of Muenster as our lecturer, and he will be speaking on “Nanopore Sequencing for Genotyping Pathogens of Tropical Diseases”.
・Date/Time: December 8(Tuesday) 5:00 pm‐6:30 pm
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Nanopore Sequencing for Genotyping Pathogens of Tropical Diseases – Bioinformatics Challenges
・Lecturer: Wojciech Makalowski（Institute of Bioinformatics, University of Muenster）
＊This lecture is transferable as a class in the medical research-related lecture course.
・Abstract: Sequencing technology continues to revolutionize life sciences. However, all the main stream technologies share several weaknesses, such as short reads and bulky instruments with high price tag. The latter prohibits usage of the sequencing directly in the field or in rural hospitals. Therefore there’s a pressing need for a simple and low-cost instrument that could be used for rapid disease diagnosis or biological sample identification. Recently introduced MinIONTM by Oxford Nanopore Technologies meets these expectations as it’s very portable with just four inches in length and operability via the USB port of a laptop computer. As a part of the Oxford Nanopore MinIONTM Access Program (MAP) we have tested applicability of the nanopore technology for genotyping of tropical diseases. In particular, it was applied to two different tasks: serotype determination of the dengue virus and genotyping of the malaria parasites. Despite very low accuracy of a single molecule read we were able successfully discriminate between different dengue virus serotypes using multiple-sequence alignment and majority rule for the base call. We demonstrate that sequence depth generated by a single run of the MinIONTM is sufficient for precise serotyping of the virus. Similarly, our preliminary results suggest that the nanopore sequencing should be useful in genotyping of the malaria parasite. Since Oxford Nanopore Technologies don’t provide any specialized software for the sequence analysis, we built a simple web-based pipeline for sero- and genotyping. The pipeline is freely available at http://bioinformatics.uni-muenster.de/tools/NanoPipe/index.hbi.
・Organizer: Yumi Yamaguchi, Masao Nagasaki